
name = "Max"
def changeName():
    name = "Niko"
    print(f"name inside the function: {name}, address = {id(name)}")
changeName()
print(f"name outside of the function: {name}, address = {id(name)}")

name inside the function: Niko, address = 4388913008
name outside of the function: Max, address = 4386289840


def add(x, y, z=0):
    return x + y + z
print(add(1, 2))
print(add(1, y=2, z=3))

3
6


def add(x, y, z=0):
    """
    Calculate the sum of up to three numbers.
    
    Parameters:
    x (int/float): The first number to be added.
    y (int/float): The second number to be added.
    z (int/float, optional): The third number to be added. Defaults to 0 if not provided.
    
    Returns:
    int/float: The sum of the numbers.
    """
    # Return the sum of the provided numbers, z is optional and defaults to 0 if not specified
    return x + y + z

import myMoudle


import pandas as pd
data = {
    'name': ['Alice', 'Bob', 'Charlie', 'David'],
    'age': [25, 30, 35, 40],
    'height': [165.4, 175.3, 168.5, 180.6]
}
df = pd.DataFrame(data)
print(df)
df[df['age'] > 30]

      name  age  height
0    Alice   25   165.4
1      Bob   30   175.3
2  Charlie   35   168.5
3    David   40   180.6


!grep "furniture.*sell" ../downloads/blocket_listings.txt

desk	furniture	sell	2000	2018-01-14
couch	furniture	sell	500	2018-10-05
shoerack	furniture	sell	200	2018-10-24
wardrobe	furniture	sell	300	2018-10-23

python retester.py


# Import module
import re


# Define a pattern
p = re.compile('ab*')
p

re.compile(r'ab*', re.UNICODE)


# Search pattern in string
p = re.compile('ab*')

p.search('abc')

<re.Match object; span=(0, 2), match='ab'>


print(p.search('cb'))

None


p = re.compile('HELLO')
m = p.search('gsdfgsdfgs  HELLO  __!@£§≈[|ÅÄÖ‚…’ﬁ]')

print(m)

<re.Match object; span=(12, 17), match='HELLO'>


# Remember, [a-z]+ matches any lower case english word
p = re.compile('[a-z]+')
result = p.search('ATGAAA')
print(result)

None


p = re.compile('[a-z]+', re.IGNORECASE)

result = p.search('ATGAAA')
result

<re.Match object; span=(0, 6), match='ATGAAA'>


p = re.compile('[a-z]+', re.IGNORECASE)

result = p.search('123 ATGAAA 456')
result

<re.Match object; span=(4, 10), match='ATGAAA'>


result.group()

'ATGAAA'


result.start()

4


result.end()

10


result.span()

(4, 10)


p = re.compile('.*HELLO.*')


m = p.search('lots of text  HELLO  more text and characters!!! ^^')


m.group()

'lots of text  HELLO  more text and characters!!! ^^'


# Find all instance of the defined pattern
p = re.compile('HELLO')
matches = p.finditer('lots of text  HELLO  more text  HELLO ... and characters!!! ^^')
print(matches)

<callable_iterator object at 0x7ff202b6efa0>


# Loop through matches
for match in matches:
    print(f'Found {match.group()} at position {match.start()}')

Found HELLO at position 14
Found HELLO at position 32


txt = "The first full stop is here: ."
pattern = re.compile('.')

match = pattern.search(txt)
print('"{}" at position {}'.format(match.group(), match.start()))

"T" at position 0


# Print all matches
matches = p.finditer(txt)
#for match in matches:
#    print('"{}" at position {}'.format(match.group(), match.start()))


# Use escape character to search
p = re.compile('\.')

m = p.search(txt)
print('"{}" at position {}'.format(m.group(), m.start()))

"." at position 29


txt = "Do it   becuase   I say so,     not becuase you want!"


# Spell the word because correctly
import re
p = re.compile('becuase')
txt = p.sub('because', txt)
print(txt)

Do it   because   I say so,     not because you want!


# Remove additional spaces
p = re.compile('\s+')
p.sub(' ', txt)

'Do it because I say so, not because you want!'

p = re.compile()

pattern = re.compile( ... )
match = pattern.search('string goes here')
if m:
    print('Match found: ', match.group())
else:
    print('No match')

fh = open('myfile.txt')
for line in fh:
    do_stuff(line)

iterations = 0
information = []

fh = open('myfile.txt', 'r')
for line in fh:
    iterations += 1
    information += do_stuff(line)

str     "hello"
int     5
float   5.2
bool    True

iterations = 0
score = 5.2

+, -, *,...   # mathematical
and, or, not  # logical 
==, !=        # (in)equality
<, >, <=, >=  # comparison
in            # membership


value = 4
nextvalue = 1
nextvalue += value
print('nextvalue: ', nextvalue, 'value: ', value)

nextvalue:  5 value:  4


x = 5
y = 7
z = 2
x > 6 and y == 7 or z > 1

True


(x > 6 and y == 7) or z > 1

True


mystr = "one"


mystr += " two" # string concatnation 
mystr

'one two'


len(mystr) # get the length

7


"one" in mystr # membership checking

True


mystr = "one"
mystr[1] = "W"

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[27], line 2
      1 mystr = "one"
----> 2 mystr[1] = "W"

TypeError: 'str' object does not support item assignment


mystr = "one"
print(mystr)
mystr = "two"
print(mystr)

one
two


mystr = "one"
print(f"mystr = {mystr}, address = {id(mystr)}")
mystr = "two"
print(f"mystr = {mystr}, address = {id(mystr)}")

mystr = one, address = 4330374000
mystr = two, address = 4414743344

s.strip()  # remove unwanted spacing

  s.split()  # split line into columns

  s.upper(), s.lower()  # change the case

p = re.compile('A.A.A')
  p.search(dnastring)

  p = re.compile('T')
  p.sub('U', dnastring)


import re

p = re.compile('p.*\sp')  # the greedy star!

p.search('a python programmer writes python code').group()

'python programmer writes p'

mylist.append('value')

value in myobj

todolist = ["work", "sleep", "eat", "work"]

todolist.sort()
todolist.reverse()
todolist[2]
todolist[-1]
todolist[2:6]


todolist = ["work", "sleep", "eat", "work"]


todolist.sort()
print(todolist)

['eat', 'sleep', 'work', 'work']


todolist.reverse()
print(todolist)

['work', 'work', 'sleep', 'eat']


todolist[2]

'sleep'


todolist[-1]

'eat'


todolist[2:]

['eat', 'work']

mydict = {"a": "alligator", "b": "bear", "c": "cat"}
counter = {"cats": 55, "dogs": 8}

mydict["a"]
mydict.keys()
mydict.values()


counter = {'cats': 0, 'others': 0}

for animal in ['zebra', 'cat', 'dog', 'cat']:
    if animal == 'cat':
        counter['cats'] += 1
    else:
        counter['others'] += 1
        
counter

{'cats': 2, 'others': 2}

myset = {"drama", "sci-fi"}

myset.add("comedy")

myset.remove("drama")


todolist = ["work", "sleep", "eat", "work"]

todo_items = set(todolist)
todo_items

{'eat', 'sleep', 'work'}


todo_items.add("study")
todo_items

{'eat', 'sleep', 'study', 'work'}


todo_items.add("eat")
todo_items

{'eat', 'sleep', 'study', 'work'}

tup = (max_length, sequence)


tup = (2, 'xy')
tup[0]

2


tup[0] = 2

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-54-874559a0c62a> in <module>
----> 1 tup[0] = 2

TypeError: 'tuple' object does not support item assignment

def find_longest_seq(file):
    # some code here...
    return length, sequence

answer = find_longest_seq(filepath)
print('length', answer[0])
print('sequence', answer[1])

answer = find_longest_seq(filepath) # return as a tuple
length, sequence = find_longest_seq(filepath) # return as two variables

if count > 10:
   print('big')
elif count > 5:
   print('medium')
else:
   print('small')


shopping_list = ['bread', 'egg', ' butter', 'milk']
tired         = True

if len(shopping_list) > 4:
    print('Really need to go shopping!')
elif not tired:
    print('Not tired? Then go shopping!')
else:
    print('Better to stay at home')

Better to stay at home

information = []
fh = open('myfile.txt', 'r')

for line in fh:
    if is_comment(line):
       use_comment(line)
    else:
       information = read_data(line)

keep_going = True
information = []
index = 0

while keep_going:
    current_line = lines[index]
    information += read_line(current_line)
    index += 1
    if check_something(current_line):
        keep_going = False


user_input = "thank god it's friday"
for letter in user_input:
    print(letter.upper())

T
H
A
N
K
 
G
O
D
 
I
T
'
S
 
F
R
I
D
A
Y


i = 0
while i < len(user_input):
    letter = user_input[i]
    print(letter.upper())
    i += 1

T
H
A
N
K
 
G
O
D
 
I
T
'
S
 
F
R
I
D
A
Y


user_input = "thank god it's friday"
for letter in user_input:

    if letter == 'd':
        break
    print(letter.upper())

T
H
A
N
K
 
G
O


# DON'T RUN THIS
i = 0
-while i < 10:    
    print(user_input[i])

  Cell In[31], line 3
    -while i < 10:
     ^
SyntaxError: invalid syntax

def prettyprinter(name, value, delim=":", end=None):
    out = "The " + name + " is " + delim + " " + value
    if end:
        out += end
    return out

""" This is a doc-string explaining what the purpose of this function/module is """

Introduction to¶

with Application to Bioinformatics¶

- Day 5¶

Day 5¶

Quiz: Review Day 4¶

1. What happens if you declare a variable with the same name inside and outside a function?¶

2. What is the difference between positional arguments and keyword arguments?¶

3. What will be the output of the following code snippet?¶

4. Why is it beneficial to use docstrings in functions?¶

Both """ and ''' can be used for docstring¶

5. How can you see the documentation of a Python library function in the console?¶

6. Which of these import statements would avoid a name conflict if there’s a local variable math in the same script?¶

7. What will happen if you import the same module multiple times in a Python script?¶

8. If you want to filter rows in df where age is greater than 30, which command would you use?¶

9. If you want to rename multiple columns in a DataFrame df, which method should you use?¶

New topic: Regular Expressions¶

Examples where regex can play a role¶

Regex is not unique for Python and it is supported by¶

Defining a search pattern¶

Common operations¶

Pattern for matching the colour family¶

Pattern for matching the different spellings¶

More common operations - classes of characters¶

More common operations - classes of characters¶

More common operations - classes of characters¶

More common operations - classes of characters¶

More common operations - classes of characters¶

[a-z] matches all letters between a and z (the english alphabet).¶

[a-z]+ matches any (lowercased) english word.¶

Example - finding patterns in a VCF file¶

Cheat sheet¶

Day 5, Exercise 1 (~30 min)¶

Practicing regular expressions¶

Take a break after the exercise (~10 min)¶

Session 2¶

Regular expressions in Python¶

Searching¶

Case insensitiveness¶

The match object¶

Zero or more...?¶

Finding all the matching patterns¶

How to find a full stop?¶

More operations¶

Substitution¶

Finally, we can fix our spelling mistakes!¶

Overview¶

Regular expressions¶

Day 5, Exercise 2 (~30 min)¶

Use regular expressions with Python¶

Take a break after the exercise (~10 min)¶

PyQuiz 5.1¶

Lunch¶

Sum up!

Processing files - looping through the lines¶

Store values¶

Values¶

Assign values¶

Compare and membership¶

Strings¶

String is immutable¶

String manipulation¶

Regular expressions help you find and replace strings.¶

Collections¶

Collections¶

Lists¶

Dictionaries¶

Sets¶

Tuples¶

Tuples in functions¶

Deciding what to do¶

Deciding what to do - if statement¶

Program flow - for loops¶

Program flow - while loops¶

Different types of loops¶

Controlling loops¶

File Input/Output¶

Input/Output¶

Code structure¶

Functions¶

Functions - keyword arguments¶

Both `"""` and `'''` can be used for docstring¶

6. Which of these import statements would avoid a name conflict if there’s a local variable `math` in the same script?¶

8. If you want to filter rows in `df` where `age` is greater than 30, which command would you use?¶

9. If you want to rename multiple columns in a DataFrame `df`, which method should you use?¶

`[a-z]` matches all letters between `a` and `z` (the english alphabet).¶

`[a-z]+` matches any (lowercased) english word.¶